still not sure if your issue is the same as mine, but I've done some more troubleshooting, see this thread, I posted some code there that might fix your issues:
posted in the wrong thread, reposting here… but TL;DR gotta re-enable buck if you disconnect from VIN while EN is low/device is off because of EN pin.
as far as I can tell, if you remove power from the boron (when it’s powered via VIN) while EN is pulled low (device “off”) and then plug it back in, it won’t resume charging while EN is still low. .
this behavior seems intermittently different if you use the actual usb port, though I’m not sure if it’s a voltage thing or what yet, haven’t gotten…